chr10-3644243-G-T

Variant names:

• chr10-3644243-G-T
• rs4881184
• ENST00000789885.1:n.467+2023C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789885.1(ENSG00000302824):​n.467+2023C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,194 control chromosomes in the GnomAD database, including 53,468 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (53468 hom., cov: 33)
• Consequence: ENSG00000302824 ENST00000789885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381
• Publications: 0 publications found

Genes affected

ENSG00000302824 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.163-104445G>T		intron_variant	Intron 1 of 1
LOC107984193	XR_001747330.2	n.338+2023C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302824	ENST00000789885.1	n.467+2023C>A		intron_variant	Intron 2 of 2
ENSG00000302824	ENST00000789886.1	n.1177+2023C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126655 AN: 152076 Hom.: 53432 Cov.: 33

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.852

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.833 AC: 126753 AN: 152194 Hom.: 53468 Cov.: 33 AF XY: 0.825 AC XY: 61389 AN XY: 74404

African (AFR) AF: 0.799 AC: 33163 AN: 41518

American (AMR) AF: 0.751 AC: 11488 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3186 AN: 3472

East Asian (EAS) AF: 0.503 AC: 2602 AN: 5176

South Asian (SAS) AF: 0.778 AC: 3752 AN: 4822

European-Finnish (FIN) AF: 0.802 AC: 8479 AN: 10566

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61170 AN: 68032

Other (OTH) AF: 0.852 AC: 1800 AN: 2112

Alfa AF: 0.875 Hom.: 242979

Bravo AF: 0.825

Asia WGS AF: 0.690 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.58
PhyloP100		0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4881184; hg19: chr10-3686435;